├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ ├── feature_request.yml │ └── question.yml └── workflows │ └── issue-autoreply.yml ├── .gitignore ├── .gitlab-ci.yml ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── bin ├── workflow-glue └── workflow_glue │ ├── __init__.py │ ├── get_reads_with_longest_aligned_ref_len.py │ ├── models │ ├── __init__.py │ ├── common.py │ └── custom.py │ ├── report.py │ ├── report_util.py │ ├── run_spoa.py │ ├── subset_reads.py │ ├── tests │ ├── __init__.py │ └── test_test.py │ ├── trim_and_qc.py │ ├── util.py │ └── wfg_helpers │ ├── __init__.py │ ├── check_bam_headers_in_dir.py │ ├── check_sample_sheet.py │ ├── check_xam_index.py │ ├── configure_igv.py │ ├── get_max_depth_locus.py │ └── reheader_samstream.py ├── data └── OPTIONAL_FILE ├── docs ├── 01_brief_description.md ├── 02_introduction.md ├── 03_compute_requirements.md ├── 04_install_and_run.md ├── 05_related_protocols.md ├── 06_input_example.md ├── 06_input_parameters.md ├── 07_outputs.md ├── 08_pipeline_overview.md ├── 09_troubleshooting.md ├── 10_FAQ.md └── 11_other.md ├── lib ├── ArgumentParser.groovy ├── CWUtil.groovy ├── NfcoreSchema.groovy ├── NfcoreTemplate.groovy ├── Pinguscript.groovy ├── WorkflowMain.groovy ├── common.nf ├── ingress.nf └── nfcore_external_java_deps.jar ├── main.nf ├── modules └── local │ ├── common.nf │ ├── de-novo.nf │ └── variant-calling.nf ├── nextflow.config ├── nextflow_schema.json ├── output_definition.json └── test_data ├── fastq-denovo-no-basecall-model ├── barcode01 │ └── reads.fastq.gz └── barcode02 │ └── reads.fastq.gz ├── fastq-denovo ├── barcode01 │ └── reads.fastq.gz └── barcode02 │ └── reads.fastq.gz ├── fastq-no-basecall-model ├── barcode01 │ └── reads.fastq.gz ├── barcode02 │ └── reads.fastq.gz └── barcode03 │ └── reads.fastq.gz ├── fastq-no-reads └── reads.fq.gz ├── fastq-single-read └── reads.fastq ├── fastq ├── barcode01 │ └── reads.fastq.gz ├── barcode02 │ └── reads.fastq.gz └── 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